This invention provides a system and method for aligning a first work piece with an underlying second work piece in the presence of occlusion by the first work piece of critical alignment features of the second work piece. The vision system, which guides the motion of a manipulator holding the first work piece and a motion stage holding the second work piece, learns secondary alignment features at least one of the first and second work pieces. Using these secondary features, the vision system determines alignment between the work pieces and guides the manipulator and the motion stage to achieve alignment as the first work piece engages the second work piece. The secondary features are used to define a course alignment. Deterministic movements of the manipulator and/or motion stage are used to learn the relationship between the secondary and primary features. Secondary features are used to direct alignment.